3HQP
Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PKL | PDB ENTRY 1PKL |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 277 | 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.31 | 62.84 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 127.486 | α = 89.73 |
| b = 151.14 | β = 80.17 |
| c = 160.319 | γ = 71.64 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | mirrors | 2008-03-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.98 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 2.3 | 41.96 | 94.7 | 0.095 | 8.2 | 1.9 | 913876 | 470114 | 2.3 | 2.3 | 41.2 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.3 | 2.42 | 90.8 | 0.638 | 1.3 | 1.3 | 65953 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PKL | 2.3 | 34.46 | 446260 | 23579 | 94.63 | 0.20111 | 0.19841 | 0.25198 | RANDOM | 42.789 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| -2.77 | 0.29 | 0.16 | -0.41 | -0.84 | 2.95 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.789 |
| r_dihedral_angle_4_deg | 16.527 |
| r_dihedral_angle_3_deg | 16.234 |
| r_dihedral_angle_1_deg | 4.96 |
| r_scangle_it | 1.391 |
| r_angle_refined_deg | 1.106 |
| r_scbond_it | 0.87 |
| r_mcangle_it | 0.492 |
| r_nbtor_refined | 0.294 |
| r_mcbond_it | 0.254 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 60784 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 4100 |
| Heterogen Atoms | 973 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| SCALA | data scaling |
